Custom rRNA Depletion kits

Order a custom riboPOOL for your species, application and sample type

Develop a custom riboPOOL for species, sample types or rRNA contaminants not covered by standard depletion kits.
Our probe-based rRNA depletion technology can be adapted to individual organisms, mixed samples, RNA-Seq and Ribosome Profiling workflows.

  • Custom designs for individual species and mixed samples
  • Compatible with intact, degraded and high-input RNA
  • Solutions for RNA-Seq, long-read sequencing and Ribo-Seq
  • Typical delivery within 3-4 weeks

Reach out to us

Download Sequence Template

When is a custom rRNA depletion kit useful?

Standard rRNA depletion kits are available for only a limited number of organisms and sample types.
A custom riboPOOL may be suitable when no established kit is available or when standard depletion does not sufficiently remove the relevant rRNA sequences.

A custom design can be used for:

  • Non-model organisms and uncommon species
  • Mixed-species and environmental samples
  • Microbiome and metatranscriptomic samples
  • Host–pathogen samples
  • Plant, fungal, bacterial and archaeal RNA
  • Degraded RNA and FFPE-derived samples
  • Persistent rRNA contaminants in Ribo-Seq libraries
  • Simultaneous depletion of rRNA from multiple organisms

What can be customized?

Requirement Customization
Species Individual organisms or defined combinations of species
Target sequences Cytoplasmic, mitochondrial and additional unwanted rRNAs
Sample composition Single-species, host–pathogen or mixed-community samples
RNA quality High-quality, degraded or FFPE-derived RNA
RNA input Standard input or high-input workflows
Application RNA-Seq, long-read sequencing or Ribo-Seq
Kit size 12, 24 or 96 reactions

How do custom riboPOOLs work?

Custom riboPOOLs use complex pools of biotinylated DNA probes designed against the targeted ribosomal RNA sequences. The probes hybridize to complementary rRNA molecules, which are subsequently captured using streptavidin-coated magnetic beads. The remaining RNA can then be used for downstream library preparation.

The probe composition is adapted to the target organism, sample composition and intended application. Unlike fixed-species depletion kits, this enables coverage of rRNA sequences specific to the investigated sample.

Step 1

The biotinylated riboPOOL probes hybdrize to target rRNAs.

Step 2

Target rRNAs are pulled down via streptavidin-coated magnetic beads.

Step 3

Purification of rRNA-depleted samples.

Custom riboPOOL Performance Data

Custom riboPOOLs have been developed for diverse eukaryotic, bacterial and archaeal species, as well as mixed samples and specialized Ribo-Seq workflows.
See some divers examples below:

Plant + divers bacterial RNA

Blood parasite RNA

Mosquito RNA

Slug RNA

How to order your custom rRNA depletion kit?

Ribo-Seq

  1. Contact us and send us your RNA sequences here
  2. We designof full coverage probes for the cytoplasmic ribosomal RNA
  3. You receive a 12 reaction preliminary kit
  4. If need for optimization: Send us your rRNA contamination data and we will adjust the oligo composition
  5. Order the final riboPOOL kit

RNA-Seq

  1. Contact us and send us your rRNA sequences here (if not available in NCBI)
  2. Place your order and choose how many reactions you need (12, 24, 96)
  3. We design your custom riboPOOL and you will receive it in 3-4 weeks

* Download our Excel sheet to add your rRNA sequences and send them directly to us at info@sitools.de.

What customers say:

"We are doing a lot of ribosome profiling experiments - mainly using mouse tissues and cell lines - and were in need of a ribosomal RNA depletion tool that was robust, economical, and adaptable. […] Hence, siTOOLs Biotech designed and produced a ribosomal RNA depletion kit depleting both extremely abundant rRNA contaminants and less abundant ones. We are very happy with the support, reactivity, and overall scientific expertise and knowledge of the siTOOLs team, which allowed us to have a great tool for a variety of experiments ongoing in the lab."

Dr. David Gatfield (University of Lausanne, Center for Integrative Genomics (CIG))

FAQ

The estimated delivery time for a custom riboPOOL is ~3-4 weeks.

We can design custom rRNA depletion kits for any species (as long as rRNA sequences are available) and any application (e.g. RNA-Seq - intact and degraded RNA, or Ribosome Profiling)

Since a custom riboPOOL is optimized for your specific species and application it generally shows higher specificity and depletion efficencies. 
Once established, the riboPOOL can be ordered as any other established kit without additional costs.